NM_001164507.2:c.1187C>T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4BP6
The NM_001164507.2(NEB):c.1187C>T(p.Ala396Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000199 in 1,610,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
Publications
- nemaline myopathy 2Inheritance: AR, AD Classification: DEFINITIVE, STRONG, LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, G2P, Ambry Genetics
- childhood-onset nemaline myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- intermediate nemaline myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- typical nemaline myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- lethal multiple pterygium syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- severe congenital nemaline myopathyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.1187C>T | p.Ala396Val | missense_variant | Exon 14 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.1187C>T | p.Ala396Val | missense_variant | Exon 14 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 | ||
NEB | ENST00000489048.1 | n.86C>T | non_coding_transcript_exon_variant | Exon 2 of 12 | 1 | |||||
NEB | ENST00000409198.5 | c.1187C>T | p.Ala396Val | missense_variant | Exon 14 of 150 | 5 | ENSP00000386259.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152020Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000285 AC: 7AN: 245442 AF XY: 0.0000225 show subpopulations
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1458690Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725544 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000118 AC: 18AN: 152020Hom.: 0 Cov.: 33 AF XY: 0.0000943 AC XY: 7AN XY: 74258 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
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not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at